This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Our laboratory makes extensive use of the Applied Biosystems API QSTAR(tm) Pulsar i QqTOF mass spectrometers for the characterization of complex biological samples obtained from collaborative research projects. During the current reporting year, several staff members have been provided training on the design and use of the QSTAR for the analysis of samples via ESI-MS/MS, MALDI-MS/MS and LC-ESI-MS/MS. They have been trained in the use of batch parameter files, processing scripts and automated IDA MS/MS functions that have been optimized for typical protein digests. LC instruction has been provided and includes theory and application of column packing methodology, LC separation parameters and ESI interfaces. Dr. Seward prepared an excellent powerpoint guide to instrument operation and data processing that is distributed to all group members when they are beginning to use these systems. After the Thermo-Fisher LTQ-Orbitrap MS system was installed in the spring of 2007, Drs. Leymarie and Infusini took on responsibility for the system, attended the Thermo training course and began to introduce other group members to its hardware and software feaures.